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- PDB-3cfo: Triple Mutant APO structure -

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Basic information

Entry
Database: PDB / ID: 3cfo
TitleTriple Mutant APO structure
ComponentsDNA polymerase
KeywordsTRANSFERASE / APO / HALF-CLOSED / OPEN / CLOSED / BASE SELECTIVITY / DNA replication / DNA-binding / DNA-directed DNA polymerase / Exonuclease / Hydrolase / Nuclease / Nucleotidyltransferase
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Monooxygenase ...DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Monooxygenase / : / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Helix Hairpins / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesBacteriophage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWang, J. / Klimenko, D. / Wang, M. / Steitz, T.A. / Konigsberg, W.H.
Citation
Journal: To be Published
Title: Insights into base selectivity from the structures of an RB69 DNA Polymerase triple mutant
Authors: Klimenko, D. / Wang, M. / Steitz, T.A. / Konigsberg, W.H. / Wang, J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Crystal structure of a POL Alpha family replicative DNA Polymerase from bacteriophage RB69
Authors: Wang, J. / Sattar, A.K. / Wang, C.C. / Karam, J.D. / Konigsberg, W.H. / Steitz, T.A. / Franklin, M.C.
#2: Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structure of the replication complex of a POL Alpha family DNA Polymerase
Authors: Franklin, M.C. / Wang, J. / Steitz, T.A.
History
DepositionMar 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0756
Polymers105,4081
Non-polymers6675
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.307, 116.424, 198.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA polymerase / Gp43


Mass: 105407.852 Da / Num. of mol.: 1 / Mutation: L561A/S565G/Y567A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage RB69 (virus) / Gene: 43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38087, DNA-directed DNA polymerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.52 Å3/Da / Density % sol: 72.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.015 M MG ACETATE, 0.05M NA CACODYLATE, 1.7 M (NH4)2SO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorDetector: CCD / Date: Jun 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 58580 / % possible obs: 98.7 % / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.099
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 1.15 / Num. unique all: 16891 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IH7

1ih7


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 19.54 / SU ML: 0.195 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23512 2620 5.1 %RANDOM
Rwork0.19153 ---
obs0.19376 49100 86.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.831 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2---1.25 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7398 0 40 257 7695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227619
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.121.96210301
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2075905
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30224.169379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.525151349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2091546
X-RAY DIFFRACTIONr_chiral_restr0.0840.21081
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025824
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.23690
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.25266
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2367
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.63424602
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.78337326
X-RAY DIFFRACTIONr_scbond_it1.64723410
X-RAY DIFFRACTIONr_scangle_it2.61532975
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 128 -
Rwork0.381 2555 -
obs--62.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.12590.42310.27873.74260.52781.7773-0.0119-0.02270.19690.3763-0.11960.83740.2633-0.21580.1315-0.1592-0.09010.1318-0.3102-0.02450.195813.05412.39356.115
21.80311.07630.46823.39130.27681.701-0.1250.07350.11510.09150.02380.1692-0.02770.08760.1013-0.1413-0.01970.0158-0.3051-0.0169-0.029934.18939.30357.3
30.89640.7323-0.31842.0432-0.39011.36740.03550.1544-0.0377-0.4642-0.03370.35120.11960.0336-0.00180.04490.0851-0.1595-0.2472-0.015-0.090230.1610.89219.01
43.1851-5.81831.071913.9273-3.86911.46790.17180.10090.1971-0.1764-0.1022-0.2003-0.0446-0.1586-0.0696-0.11980.1065-0.0543-0.26420.00020.042610.37634.07832.806
55.16933.38043.4833.58131.30463.0375-0.0098-0.36290.406-0.3689-0.11620.0610.0465-0.24080.1259-0.02190.08480.0322-0.20740.0295-0.153539.54830.30122.924
60.90350.51231.05142.72180.97094.25270.0060.05910.08230.24130.1576-0.32970.26730.0249-0.1636-0.04310.05530.0814-0.30950.0266-0.074361.17534.60735.447
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1051 - 105
2X-RAY DIFFRACTION1AA340 - 389340 - 389
3X-RAY DIFFRACTION2AA106 - 339106 - 339
4X-RAY DIFFRACTION3AA390 - 468390 - 468
5X-RAY DIFFRACTION3AA576 - 706576 - 706
6X-RAY DIFFRACTION4AA469 - 575469 - 575
7X-RAY DIFFRACTION5AA707 - 737707 - 737
8X-RAY DIFFRACTION6AA738 - 903738 - 903

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